Work

A Transcriptome-Wide Association Study Among 97,898 Women to Identify Candidate Susceptibility Genes for Epithelial Ovarian Cancer Risk

Year: 2018
Type: article
Study design: Observational Study
Abstract: Large-scale genome-wide association studies (GWAS) have identified approximately 35 loci associated with epithelial ovarian cancer (EOC) risk. The majority of GWAS-identified disease susceptibility variants are located in noncoding regions, and causal genes underlying these associations remain largely unknown. Here, we performed a transcriptome-wide association study to search for novel genetic loci and plausible causal genes at known GWAS loci. We used RNA sequencing data (68 normal ovarian tissue samples from 68 individuals and 6,124 cross-tissue samples from 369 individuals) and high-density genotyping data from European descendants of the Genotype-Tissue Expression (GTEx V6) project to build ovarian and cross-tissue models of genetically regulated expression using elastic net methods. We evaluated 17,121 genes for their cis-predicted gene expression in relation to EOC risk using summary statistics data from GWAS of 97,898 women, including 29,396 EOC cases. With a Bonferroni-corrected significance level of P < 2.2 × 10−6, we identified 35 genes, including FZD4 at 11q14.2 (Z = 5.08, P = 3.83 × 10−7, the cross-tissue model; 1 Mb away from any GWAS-identified EOC risk variant), a potential novel locus for EOC risk. All other 34 significantly associated genes were located within 1 Mb of known GWAS-identified loci, including 23 genes at 6 loci not previously linked to EOC risk. Upon conditioning on nearby known EOC GWAS-identified variants, the associations for 31 genes disappeared and three genes remained (P < 1.47 × 10−3). These data identify one novel locus (FZD4) and 34 genes at 13 known EOC risk loci associated with EOC risk, providing new insights into EOC carcinogenesis. Significance: Transcriptomic analysis of a large cohort confirms earlier GWAS loci and reveals FZD4 as a novel locus associated with EOC risk. Cancer Res; 78(18); 5419–30. ©2018 AACR.
Authors: Yingchang Lu, Alicia Beeghly-Fadiel, Lang Wu, Xingyi Guo, Bingshan Li, Joellen M. Schildkraut, Hae Kyung Im, Yian A. Chen, Jennifer B. Permuth, Brett M. Reid, Jamie K. Teer, Kirsten B. Moysich, Irene L. Andrulis, Hoda Anton-Culver, Banu K. Arun, Elisa V. Bandera, Rosa B. Barkardottir, Daniel R. Barnes, Javier Benitez, Line Bjorge, James Brenton, Ralf Butzow, Trinidad Caldes, Maria A. Caligo, Ian Campbell, Jenny Chang-Claude, Kathleen B.M. Claes, Fergus J. Couch, Daniel W. Cramer, Mary B. Daly, Anna deFazio, Joe Dennis, Orland Diez, Susan M. Domchek, Thilo Dörk, Douglas F. Easton, Diana M. Eccles, Peter A. Fasching, Renée T. Fortner, George Fountzilas, Eitan Friedman, Patricia A. Ganz, Judy Garber, Graham G. Giles, Andrew K. Godwin, David E. Goldgar, Marc T. Goodman, Mark H. Greene, Jacek Gronwald, Ute Hamann, Florian Heitz, Michelle A.T. Hildebrandt, Claus K. Høgdall, Antoinette Hollestelle, Peter J. Hulick, David G. Huntsman, Evgeny N. Imyanitov, Claudine Isaacs, Anna Jakubowska, Paul James, Beth Y. Karlan, Linda E. Kelemen, Lambertus A. Kiemeney, Susanne K. Kjaer, Ava Kwong, Nhu D. Le, Goska Leslie, Fabienne Lesueur, Douglas A. Levine, Amalia Mattiello, Taymaa May, Lesley McGuffog, Iain A. McNeish, Melissa A. Merritt, Francesmary Modugno, Marco Montagna, Susan L. Neuhausen, Heli Nevanlinna, Finn C. Nielsen, Liene Nikitina-Zake, Robert L. Nussbaum, Kenneth Offit, Edith Olah, Olufunmilayo I. Olopade, Sara H. Olson, Håkan Olsson, Ana Osorio, Sue K. Park, Michael T. Parsons, Petra H.M. Peeters, Tanja Pejovic, Paolo Peterlongo, Catherine M. Phelan, Miquel Angel Pujana, Susan J. Ramus, Gad Rennert, Harvey Risch, Gustavo C. Rodriguez, Cristina Rodríguez-Antona, Isabelle Romieu, Matti A. Rookus, Mary Anne Rossing, Iwona K. Rzepecka, Dale P. Sandler, Rita K. Schmutzler, Veronica W. Setiawan, Priyanka Sharma, Weiva Sieh, Jacques Simard, Christian F. Singer, Honglin Song, Melissa C. Southey, Amanda B. Spurdle, Rebecca Sutphen, Anthony J. Swerdlow, Manuel R. Teixeira, Soo H. Teo, Mads Thomassen, Marc Tischkowitz, Amanda E. Toland, Antonia Trichopoulou, Nadine Tung, Shelley S. Tworoger, Elizabeth J. van Rensburg, Adriaan Vanderstichele, Ana Vega, Digna Velez Edwards, Penelope M. Webb, Jeffrey N. Weitzel, Nicolas Wentzensen, Emily White, Alicja Wolk, Anna H. Wu, Drakoulis Yannoukakos, Kristin K. Zorn, Simon A. Gayther, Antonis C. Antoniou, Andrew Berchuck, Ellen L. Goode, Georgia Chenevix-Trench, Thomas A. Sellers, Paul D.P. Pharoah, Wei Zheng, Jirong Long
Institutions: Vanderbilt University, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, University of Virginia, University of Chicago, Moffitt Cancer Center, Roswell Park Comprehensive Cancer Center, Mount Sinai Hospital, University of Toronto, Lunenfeld-Tanenbaum Research Institute, University of California, Irvine, The University of Texas MD Anderson Cancer Center, Rutgers Cancer Institute, University of Iceland, National University Hospital of Iceland, University of Cambridge, Spanish National Cancer Research Centre, Centre for Biomedical Network Research on Rare Diseases, Haukeland University Hospital, University of Bergen, Cancer Research UK Cambridge Center, University of Helsinki, Helsinki University Hospital, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos, Centro de Investigación Biomédica en Red de Cáncer, University of Pisa, Azienda Ospedaliera Universitaria Pisana, The University of Melbourne, Peter MacCallum Cancer Centre, German Cancer Research Center, University Medical Center Hamburg-Eppendorf, University Cancer Center Hamburg, Ghent University, Mayo Clinic, Brigham and Women's Hospital, Harvard University, Fox Chase Cancer Center, The University of Sydney, Westmead Hospital, Westmead Institute for Medical Research, Vall d'Hebron Institute of Oncology, Abramson Cancer Center, University of Pennsylvania, Medizinische Hochschule Hannover, University of Southampton, University of California, Los Angeles, Friedrich-Alexander-Universität Erlangen-Nürnberg, Universitätsklinikum Erlangen, Comprehensive Cancer Center Erlangen, Aristotle University of Thessaloniki, Papageorgiou General Hospital, Tel Aviv University, Sheba Medical Center, UCLA Jonsson Comprehensive Cancer Center, Dana-Farber Cancer Institute, Cancer Council Victoria, Monash University, University of Kansas Medical Center, University of Utah, Huntsman Cancer Institute, Cedars-Sinai Medical Center, National Cancer Institute, Division of Cancer Epidemiology and Genetics, Pomeranian Medical University, Helios Dr. Horst Schmidt Kliniken Wiesbaden, Kliniken Essen-Mitte, University of Copenhagen, Rigshospitalet, Erasmus MC Cancer Institute, Endeavor Health, BC Cancer Agency, University of British Columbia, Vancouver General Hospital, Institute of Oncology NN Petrov, Georgetown University, Georgetown Lombardi Comprehensive Cancer Center, Medical University of South Carolina, Radboud University Nijmegen, Radboud University Medical Center, Radboud Institute for Health Sciences, Danish Cancer Society, Hong Kong Sanatorium and Hospital, University of Hong Kong, Inserm, Université Paris Sciences et Lettres, École Nationale Supérieure des Mines de Paris, Institut Curie, Memorial Sloan Kettering Cancer Center, NYU Langone Health, NYU Langone’s Laura and Isaac Perlmutter Cancer Center, Federico II University Hospital, University of Naples Federico II, University Health Network, Princess Margaret Cancer Centre, University of Glasgow, University of Hawaii Cancer Center, Imperial College London, University of Pittsburgh, Magee-Womens Research Institute, UPMC Hillman Cancer Center, Istituto Oncologico Veneto, City of Hope, Beckman Research Institute, Copenhagen University Hospital, Latvian Biomedical Research and Study Centre, University of California, San Francisco, National Institute of Oncology, Lund University, Seoul National University, QIMR Berghofer Medical Research Institute, Utrecht University, University Medical Center Utrecht, Oregon Health & Science University, IFOM, Institut d'Investigació Biomédica de Bellvitge, Institut Català d'Oncologia, Garvan Institute of Medical Research, UNSW Sydney, The Kinghorn Cancer Centre, Technion – Israel Institute of Technology, Carmel Medical Center, Yale University, Centre international de recherche sur le cancer, The Netherlands Cancer Institute, University of Washington, Fred Hutch Cancer Center, The Maria Sklodowska-Curie National Research Institute of Oncology, National Institutes of Health, National Institute of Environmental Health Sciences, University of Cologne, University Hospital Cologne, University of Southern California, Icahn School of Medicine at Mount Sinai, Centre hospitalier universitaire de Québec, Université Laval, Comprehensive Cancer Center Vienna, Medical University of Vienna, University of South Florida, Institute of Cancer Research, Universidade do Porto, Instituto Português de Oncologia Francisco Gentil, Instituto de Ciências Biomédicas Albel Salazar, University Malaya Medical Centre, University of Malaya, Cancer Research Malaysia, Odense University Hospital, McGill University, The Ohio State University, National and Kapodistrian University of Athens, Hellenic Health Foundation, Beth Israel Deaconess Medical Center, University of Pretoria, Universitair Ziekenhuis Leuven, Fundación Pública Galega de Medicina Xenómica, City Of Hope National Medical Center, Karolinska Institutet, National Centre of Scientific Research "Demokritos", Magee-Womens Hospital, Duke University, Duke Medical Center
Language: English
Subfield: Genetics
Open Access status: bronze
Funders: U.S. Department of Defense, Oak Foundation, Ovarian Cancer Research Fund, Roswell Park Cancer Institute, Minnesota Ovarian Cancer Alliance, World Health Organization, State of Connecticut Department of Public Health, Vanderbilt University, Oregon Health and Science University, Mayo Foundation for Medical Education and Research, Rutgers Cancer Institute of New Jersey, Kræftens Bekæmpelse, Deutsches Krebsforschungszentrum, Centre International de Recherche sur le Cancer, Kreftforeningen, Moffitt Cancer Center, Cancer Research Society, Wellcome Trust, Ovarian Cancer Australia, Swedish Cancer Foundation, Vanderbilt University Medical Center, Georgia Clinical and Translational Science Alliance, Fred C. and Katherine B. Andersen Foundation, Lon V. Smith Foundation, Cancer Research UK, National Institute for Health and Care Research, University of Cambridge, University College London, European Commission, Cancer Australia, Cancer Institute NSW, Institut National de la Santé et de la Recherche Médicale, Radboud Universiteit, Bundesministerium für Bildung und Forschung, Cancerfonden, Canadian HIV Trials Network, Canadian Institutes of Health Research, Ministerio de Economía y Competitividad, Ministry of Health, Labour and Welfare, Korea Health Industry Development Institute, Ligue Contre le Cancer, Helse Vest, Vetenskapsrådet, NordForsk, Associazione Italiana per la Ricerca sul Cancro, Norges Forskningsråd, Deutsche Krebshilfe, Institut Gustave-Roussy, Mutuelle Générale de l'Education Nationale, Pomorski Uniwersytet Medyczny W Szczecinie, Hebei Medical University, BC Cancer Foundation, Hellenic Health Foundation, Peter MacCallum Foundation, National Institutes of Health, Health Canada, Canadian Institutes of Health Research, Medical Research Council, World Cancer Research Fund, National Health and Medical Research Council, Cancer Council Victoria, Japan Society for the Promotion of Science, Instituto de Salud Carlos III, NIHR Cambridge Biomedical Research Centre, National Cancer Institute, National Center for Research Resources, National Center for Advancing Translational Sciences, European Social Fund, Medical Research and Materiel Command, State of Florida
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OpenAlex ID: W2883813435
FWCI: 5.415
Cites: 50
Cited by: 67
Related to: 10